Using our allele-specific PCR (ASP) assay, which allows detection and quantification of rare mutations at levels as low as 0.1% in a virus population, we are performing studies designed to understand the dynamics of appearance and disappearance of NNRTI resistance mutations in patients starting and stopping therapy as well as in drug-naive patients. In collaboration with Dr. Mellors, we are assessing the impact of low-frequency mutations on subsequent treatment failure. In collaboration with Drs. Lynn Morris (South Africa) and Pat Robertson (Boehringer Ingelheim), we are also analyzing the rise and fall of NNRTI resistance mutations in women exposed to single-dose nevirapine to prevent mother-to-infant transmission, and to assess the consequences of these mutations for subsequent nevirapine-based therapy. In collaboration with John Mellors, the HVIB completed analysis of samples from a large prospective, randomized clinical trial, ACTG 5208. The OCTANE/A5208 study of combination antiretroviral therapy in women who had previously taken single dose nevirapine to prevent mother to child transmission. Women were randomized to receive combination therapy with nevirapine or comparator protease inhibitor, lopinavir/ritonavir. The study was stopped early because significantly more women in the nevirapine arm (26%) than in the lopinavir /ritonavir arm (8%) reached the primary endpoint of virologic failure or death (P = 0.0004). Detection of NNRTI resistance in entry samples by standard genotype was strongly associated with failure in the nevirapine arm, but more than half of endpoints occurred in women with negative standard genotypes. To test the hypothesis that low frequency NNRTI-resistant variants were responsible, in part, for excessive failure in the nevirapine arm, we used allele-specific polymerase chain reaction (ASP) to detect and quantify nevirapine-resistant variants at study entry. Standard genotype and ASP results from entry samples were obtained in 232 of the 241 women who received randomized therapy. By allele specific PCR, we detected NNRTI-resistant variants in 35% of women with negative standard genotype and were associated with higher risk of failure of nevirapine-containing antiretroviral therapy across the entire range of mutants frequencies detected (0.3% to greater than 30%). Standard resistance testing did not identify the majority of women at increased risk for failure of nevirapine-containing antiretroviral therapy after single dose nevirapine. These findings (ms in preparartion) suggest that even low levels of resistance are associated with regimen failure, and have wide ranging consequences for therapeutic choices for women with a history of single dose nevirapine to prevent mother to child transmission. With Dr. Vineet KewalRamani, we are assessing the appearance of NNRTI resistance mutations in a pigtail macaque model of infection with SIV containing HIV RT (RT-SHIV) and treated with efavirenz, as a model for the evolution of resistance in humans so treated. In collaboration with Dr. Eric Freed, we are developing a sensitive assay for the duplication of the PTAP motif in the p6 portion of Gag frequently found in association with drug resistance. An advanced version of the allele-specific PCR assay is currently under development to increase the sensitivity of mutant detection 10-100 fold. As a result, the new assay will approach detection of mutations occurring at a frequency that approximates the HIV-1 reverse transcriptase mutation rate.We will, therefore, be able to determine with great sensitivity the relative levels of drug resistance mutations present prior to drug initiation. These studies will be essential in understanding the relative level of pre-existing drug resistance that contributes to subsequent drug failure during antiretroviral therapy. We are also using this approach investigating the impact of drug resistance mutations in HIV-1 infected population over time With H.C. Lane and R. Davey (NIAID), we are investigating the presence of drug resistance mutations in samples obtained relatively early in the epidemic (1988-1990) prior to the widespread introduction of antiretroviral therapy . As a result, we will be able to determine the relative prevalence of HIV-1 mutations in the absence of any potential effect of antiretroviral therapy. These studies will be particularly useful in understanding the role of drug resistance that is transmitted at the time of infection. Comparison of the relative level of drug resistance mutations in samples from patients from pre-antiretroviral era with those obtained from contemporary drug nave populations will offer new insights on the influence of transmitted drug resistance on the overall prevalence of drug resistance. In addition we are collaborating with D. Richman (University of California, San Diego) to investigate the presence and duration of drug resistance mutations in patients with transmitted drug resistance. [Corresponds to Project 3 in the April 2007 site visit report of the Host-Virus Interaction Branch, HIV Drug Resistance Program]